def __init__(self,
gff_file,
fp=None,
gffdataline=GFFDataLine,
format='gff'):
# Storage for format info
self._format = format
self._version = None
# Initialise empty TabFile
TabFile.__init__(self,
None,
fp=None,
tab_data_line=GFFDataLine,
column_names=GFF_COLUMNS)
# Populate by iterating over GFF file
for line in GFFIterator(gff_file=gff_file,
fp=fp,
gffdataline=gffdataline):
if line.type == ANNOTATION:
# Append to TabFile
self.append(tabdataline=line)
elif line.type == PRAGMA:
# Try to extract relevant data
pragma = str(line)[2:].split()
if pragma[0] == 'gff-version':
self._version = pragma[1]
def __init__(self, gff_file, fp=None, gffdataline=GFFDataLine, format="gff"):
# Storage for format info
self._format = format
self._version = None
# Initialise empty TabFile
TabFile.__init__(self, None, fp=None, tab_data_line=GFFDataLine, column_names=GFF_COLUMNS)
# Populate by iterating over GFF file
for line in GFFIterator(gff_file=gff_file, fp=fp, gffdataline=gffdataline):
if line.type == ANNOTATION:
# Append to TabFile
self.append(tabdataline=line)
elif line.type == PRAGMA:
# Try to extract relevant data
pragma = str(line)[2:].split()
if pragma[0] == "gff-version":
self._version = pragma[1]
def __init__(self,infile,column_names):
"""Create a new BedMaker instance
Arguments:
infile: tab-delimited data file to read initial data from
column_names: names to assign to data columns read in from the file
"""
# Initialise base class
TabFile.__init__(self,infile,column_names=column_names)
# Check if first line is real data
if len(self) > 0:
if not self[0]['start'].isdigit() or \
not self[0]['stop'].isdigit():
print "First line of input file doesn't look like data, removing"
del(self[0])
# Remove blank lines
i = 0
while i < len(self):
if not str(self[i]).strip():
del(self[i])
else:
i += 1
